And in fact it is not, and even in the article it is U+09CE. One codepoint. If his input method irks him, he's as free to tweak it as I am to switch to Dvorak.
Also folks, there's no "CJK unification" project. It's Han unification. Han characters are Han characters, just like Latin characters are Latin characters. Just because German has ß and Danish has Ø doesn't mean A isn't a Latin character and not, say, a French one. Not to get all Ayn Rand-y, but A is A is U+0041 in all Western European/Latin alphabets. It makes sense for 中国 and 日本to have the same encoding in Chinese and Japanese.
Yes, there are some frustrating issues -- it has been historically difficult to set priorities for fonts in X and since Chinese fonts tend to have more glyphs, you often wind up with Chinese glyphs when you wanted Japanese glyphs. But this is not an encoding issue. Localization/Internationalization is really difficult. Making a separate code point for every glyph is not going to change that for the better.
Frankly, this is irrelevant to the actual problem, which is the input system, and which has nothing to do with Unicode. Nothing prevents a single key from typing multiple codepoints at once.